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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 19, 2021 |
| Title |
F1 |
| Sample type |
SRA |
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| Source name |
female_room-air_lung
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| Organism |
Mus musculus |
| Characteristics |
exposure: room-air
strain: C57BL/6
Sex: female
tissue: lung
platform: 10x Genomics
technology: Chromium Single Cell 3' Kits (v3 Chemistry)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lungs were removed and single cells dissociated using collagenase and elastase.
Single-cell libraries were prepared using the standard 10x Genomics single cell 3' reagent kits v3 processing workflow.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
F1_S1_L001
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| Data processing |
fastq read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 25 bp long were discarded.
Downstream processing was conducted with STAR v2.7.3a and its single cell seq implementation "STARsolo".
Cells being accepted had to pass the following filters: at least 750 transcripts profiled, having at least 10% of transcripts arising from intron spanning or unspliced reads, less than 15% of their transcriptome of mitochondrial origin
Genome_build: GRCm38.p6
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| Submission date |
Mar 04, 2021 |
| Last update date |
Nov 19, 2021 |
| Contact name |
John McDonough |
| Organization name |
Yale School of Medicine
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| Street address |
300 Cedar St
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE168299 |
Cell-Specific Transcriptome of the COPD Alveolar Niche |
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| Relations |
| BioSample |
SAMN18144527 |
| SRA |
SRX10241388 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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